rs12962411

Variant names:

• chr18-31811560-G-A
• rs12962411

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.071 in 152,202 control chromosomes in the GnomAD database, including 401 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.071 (401 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10804 AN: 152084 Hom.: 402 Cov.: 32

Gnomad AFR AF: 0.0578

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0546

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0723

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0791

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0710 AC: 10807 AN: 152202 Hom.: 401 Cov.: 32 AF XY: 0.0704 AC XY: 5242 AN XY: 74430

Gnomad4 AFR AF: 0.0578

Gnomad4 AMR AF: 0.0640

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0545

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.0723

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0798 Hom.: 703

Bravo AF: 0.0708

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12962411; hg19: chr18-29391523;